Fix/thicknesses_

.github/workflows/CD.yml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Build SDist
         run: |
-          pip install build
+          pip install build 
           python -m build
 
       - uses: actions/upload-artifact@v4
@@ -112,6 +112,7 @@ jobs:
     name: Test wheels on ${{ matrix.os }}
     needs: pypi-build-wheels
     runs-on: ${{ matrix.os }}
+    if : github.ref == 'refs/heads/master'
     strategy:
       fail-fast: false
       matrix:
@@ -162,6 +163,7 @@ jobs:
   conda-build:
     name: Conda Build and Deploy ${{ matrix.os }} - Python Version-${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
+    if : github.ref == 'refs/heads/master'
     strategy:
       fail-fast: false
       matrix:
@@ -225,6 +227,7 @@ jobs:
 
   documentation-test:
     runs-on: ubuntu-latest
+    if: github.ref == 'refs/heads/master'
     steps:
       - uses: actions/checkout@v4
       - run: |
@@ -240,7 +243,8 @@ jobs:
   documentation-deploy:
     runs-on: ubuntu-latest
     needs: [release-please, documentation-test]
-    if: ${{ needs.release-please.outputs.release_created }}
+    if: ${{ needs.release-please.outputs.release_created }} && github.ref == 'refs/heads/master'
+
     steps:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4

MANIFEST.in

@@ -1,2 +1,8 @@
+include LICENSE
+include README.md 
+
 include map2loop/_datasets/clut_files/*.csv
-include map2loop/_datasets/config_files/*.json
+include map2loop/_datasets/config_files/*.json
+include map2loop/_datasets/geodata_files/hamersley/*
+
+recursive-include tests *.py

README.md

@@ -1,4 +1,4 @@
-# Map2Loop 3.0
+# Map2Loop 3.1
 
 Generate 3D geological model inputs from geological maps — a high-level implementation and extension of the original map2loop code developed by Prof. Mark Jessell at UWA. To see an example interactive model built with map2loop and LoopStructural, follow this link:
 
@@ -23,12 +23,20 @@ conda config --add channels conda-forge
 
 ### Run
 
-To just use map2loop, issue the following
+To just use map2loop, issue the following. <sup>*</sup>
 
 ```bash
-conda install -c conda-forge -c loop3d map2loop -y
+git clone https://github.com/Loop3D/map2loop.git
+
+cd map2loop
+
+conda install -c loop3d --file dependencies.txt
+
+pip install .
 ```
 
+<p><sup>*</sup> We're actively working towards a better approach - stay tuned! </p>
+
 ### Documentation
 
 If you can call it that, is available <a href="https://loop3d.org/map2loop/">here</a>

dependencies.txt

@@ -5,7 +5,8 @@ shapely
 networkx
 owslib
 map2model
-loopprojectfile==0.1.3
+hjson
+loopprojectfile==0.1.4
 beartype
 gdal==3.8.4
 hjson

docs/Dockerfile

@@ -12,8 +12,8 @@ RUN apt-get update -qq && \
     libgl1\
     libtinfo5\
     libtiff6\
-    libgl1-mesa-glx
-
+    libgl1-mesa-glx\
+    libarchive13
 
 COPY . /map2loop 
 

docs/docker-compose.yml

@@ -1,5 +1,3 @@
-version: "3"
-
 services:
   map2loop:
     build:

docs/source/_static/m2l_code_template.ipynb

@@ -46,7 +46,7 @@
     "from map2loop.m2l_enums import VerboseLevel\n",
     "from map2loop.m2l_enums import Datatype\n",
     "from map2loop.sampler import SamplerSpacing, SamplerDecimator\n",
-    "from map2loop.sorter import SorterUseHint, SorterUseNetworkX, SorterAgeBased, SorterAlpha\n",
+    "from map2loop.sorter import SorterAlpha\n",
     "import time"
    ]
   },

map2loop/__init__.py

@@ -1,2 +1,118 @@
 from .project import Project
 from .version import __version__
+
+import warnings  # TODO: convert warnings to logging
+from packaging import version as pkg_version  # used instead of importlib.version because adheres to PEP 440 using pkg_version.parse
+import pathlib
+import re
+import pkg_resources #import get_distribution, DistributionNotFound  # Use pkg_resources for version checking
+
+class DependencyChecker:
+    '''
+    A class to check installation and version compatibility of each package in dependencies.txt
+
+    Attributes:
+    package_name (str): Name of the package
+    dependency_file (str): path to dependencies.txt
+    required_version (str or None): required version of the package as in dependencies.txt
+    installed_version (str or None): installed version of the package in the current environment
+    '''
+
+    def __init__(self, package_name, dependency_file="dependencies.txt"):
+
+        self.package_name = package_name
+        self.dependency_file = pathlib.Path(__file__).parent.parent / dependency_file
+        self.required_version = self.get_required_version()
+        self.installed_version = self.get_installed_version()
+
+    ## 1) get required version of each dependency from dependencies.txt
+    def get_required_version(self):
+        '''
+        Get the required package version for each package from dependencies.txt; 
+
+        Returns:
+            str or None: The required version of the package (if specified), otherwise None.
+        '''
+        try:
+            with self.dependency_file.open("r") as file:
+                # search for the dependency line in dependencies.txt
+                for line in file:
+                    if line.startswith(f"{self.package_name}=="):
+                        match = re.match(rf"^{self.package_name}==([\d\.]+)", line.strip())
+                        if match:
+                            return match.group(1)  # get the version if found
+                    elif line.strip() == self.package_name:
+                        # dependency listed without a version
+                        return None
+                # if dependency line not found in dependencies.txt (shouldn't happen, but just in case)
+                print(f"{self.package_name} version not found in {self.dependency_file}.")
+        except FileNotFoundError:  # in case dependencies.txt is not found (shouldn't happen)
+            warnings.warn(
+                f"{self.dependency_file} not found. Unable to check {self.package_name} version compatibility.",
+                UserWarning
+            )
+        return None
+
+    ## 2) Check the installed version of the dependency and compare with required version
+    def get_installed_version(self):
+        '''
+        Get the installed version of the package.
+
+        Returns:
+            str: The installed version of the package.
+        '''
+        try:
+            # Get installed version of the package using pkg_resources
+            return pkg_resources.get_distribution(self.package_name).version
+        except pkg_resources.DistributionNotFound:
+            # Raise ImportError if package is not installed
+            raise ImportError(f"{self.package_name} is not installed. Please install {self.package_name}.")
+
+    ## 3) Compare the installed version of the dependency with the required version, if applicable
+    def check_version(self):
+        '''
+        Checks if the installed version of the package matches the required version uin the dependencies.txt file.
+
+        '''
+        if self.required_version is None:
+            # No required version specified, only check if installed
+            if self.installed_version is None:
+                raise ImportError(f"{self.package_name} is not installed. Please install {self.package_name} before using map2loop.")
+            # else:
+            #     print(f"{self.package_name} is installed.")
+        else:
+            # Compare versions if required version is specified
+            if self.installed_version is None or pkg_version.parse(self.installed_version) != pkg_version.parse(self.required_version):
+                raise ImportError(
+                    f"Installed version of {self.package_name}=={self.installed_version} does not match required version=={self.required_version}. "
+                    f"Please install the correct version of {self.package_name}."
+                )
+
+            # else:
+            #     print(f"{self.package_name} version is compatible.")
+
+# check all dependencies & versions in dependencies.txt
+def check_all_dependencies(dependency_file="dependencies.txt"):
+    dependencies_path = pathlib.Path(__file__).parent.parent / dependency_file
+    try:
+        with dependencies_path.open("r") as file:
+            for line in file:
+                line = line.strip()
+                # skip the gdal line
+                if line.startswith("gdal"):
+                    continue
+                if line:
+                    # separate package name and version (if available)
+                    if "==" in line:
+                        package_name, _ = line.split("==")
+                    else:
+                        package_name = line
+
+                    # check version for each package
+                    checker = DependencyChecker(package_name, dependency_file=dependency_file)
+                    checker.check_version()
+    except FileNotFoundError:
+        ImportError(f"{dependency_file} not found. No dependencies checked for map2loop", UserWarning)
+
+# Run check for all dependencies listed in dependencies.txt
+check_all_dependencies()

map2loop/_datasets/config_files/NSW.json

@@ -24,7 +24,7 @@
         "intrusive_text": "intrusive",
         "volcanic_text": "volcanic",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]},
+        "ignore_lithology_codes": ["cover"]},
     "fault": {
         "structtype_column": "boundaryty",
         "fault_text": "Fault",
@@ -36,7 +36,7 @@
         "dipestimate_column": "faultdipan",
         "dipestimate_text": "Moderate,Listric,Steep,Vertical",
         "name_column": "name",
-        "objectid_column": "unique_id"
+        "objectid_column": "unique_id", 
     },
     "fold": {
         "structtype_column": "codedescpt",

map2loop/_datasets/config_files/QLD.json

@@ -24,7 +24,7 @@
         "intrusive_text": "Y",
         "volcanic_text": "VOLCANIC",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]
+        "ignore_lithology_codes": ["cover"]
     },
     "fault": {
         "structtype_column": "type",

map2loop/_datasets/config_files/SA.json

@@ -24,7 +24,7 @@
         "intrusive_text": "intrusive",
         "volcanic_text": "volc",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]
+        "ignore_lithology_codes": ["cover"]
     },
     "fault": {
         "structtype_column": "descriptio",

map2loop/_datasets/config_files/TAS.json

@@ -24,7 +24,7 @@
         "intrusive_text": "granit",
         "volcanic_text": "volc",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]
+        "ignore_lithology_codes": ["cover"]
     },
     "fault": {
         "structtype_column": "TYPE",

map2loop/_datasets/config_files/VIC.json

@@ -24,7 +24,7 @@
         "intrusive_text": "intrusion",
         "volcanic_text": "volc",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]
+        "ignore_lithology_codes": ["cover"]
     },
     "fault": {
         "structtype_column": "featuretyp",

map2loop/_datasets/config_files/WA.json

@@ -24,7 +24,7 @@
         "intrusive_text": "intrusive",
         "volcanic_text": "volcanic",
         "objectid_column": "ID",
-        "ignore_codes": ["cover"]
+        "ignore_lithology_codes": ["cover"]
     },
     "fault": {
         "structtype_column": "feature",